Allogeneic or Haploidentical Stem Cell Transplant Followed By High-Dose Cyclophosphamide in Treating Patients With Relapsed or Refractory Acute Myeloid Leukemia

Inclusion Criteria:

* AML without complete remission (CR/CRc/CRi) after at least 2 induction therapies OR
* AML that has relapsed within 6 months after obtaining a CR OR
* AML that has relapsed more than 6 months after obtaining a CR, and has treatment failure (TF) or progressive disease (PD) following at least 1 re-induction regimen OR
* AML that has relapsed post Allogeneic transplantation
* Active AML (bone marrow blasts ≥ 5% by morphology, staining, or flow) and/or presence of estramedullary disease
* Available HLA-haploidentical donor that meets the following criteria:

  * Blood-related family member (sibling (full or half), offspring, or parent, cousin, niece or nephew, aunt or uncle, or grandparent)
  * At least 18 years of age
  * HLA-haploidentical donor/recipient match by at least low-resolution typing per institutional standards
  * In the investigator's opinion, is in general good health, and medically able to tolerate leukapheresis required for harvesting HSC
  * No active hepatitis
  * Negative for HTLV and HIV
  * Not pregnant

NOTE: there were HLA-matched sibling and HLA-matched unrelated donor cohorts, but those closed without completion of accrual with Amendment 11

* Karnofsky performance status ≥ 50 %
* Adequate organ function as defined below:

  * Total bilirubin ≤ 2.5 mg/dl (unless the patient has a history of Gilbert's syndrome)
  * AST(SGOT) and ALT(SGPT) ≤ 3.0 x IULN
  * Creatinine ≤ 2.0 x IULN OR estimated creatinine clearance ≥ 30 mL/min/1.73 m2 by Cockcroft-Gault Formula
  * Oxygen saturation ≥ 90% on room air
  * LVEF ≥ 40%
  * FEV1 and FVC ≥ 40% predicted, DLCOc ≥ 40% predicted. If DLCO is \< 40%, patients will still be considered eligible if deemed safe after a pulmonary evaluation.
* At least 18 years of age at the time of study registration
* Able to understand and willing to sign an IRB approved written informed consent document (or that of legally authorized representative, if applicable)

Exclusion Criteria:

* Circulating blast count ≥ 10,000/uL by morphology or flow cytometry (cytoreductive therapies including leukapheresis or hydroxyurea are allowed)
* Known HIV or Active hepatitis B or C infection
* Known hypersensitivity to one or more of the study agents
* Currently receiving or has received any investigational drugs within the 14 days prior to the first dose of study drug (Day -7)
* Currently receiving or has received any intensive chemotherapy within the 14 days prior to the first dose of study drug (Day -7) (hydrea or other non-intensive regimens such as decitabine may be used but must stop at least one day prior to the first dose of study drug)
* Pregnant and/or breastfeeding
* Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, unstable cardiac arrhythmias, or psychiatric illness/social situations that would limit compliance with study requirements.